| 4_1hfypdb |
| ID: | 1516869569 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 120 (114) | ||
| Sequences: | 581 (339.4) | ||
| Seq/Len: | 5.096 | ||
| Nf(neff/√len): | 31.8 |
HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 5.096).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 82_D | 88_D | 3.586 | 1.00 |
| 82_D | 87_D | 2.696 | 1.00 |
| 75_I | 80_F | 2.443 | 1.00 |
| 30_A | 52_L | 2.202 | 1.00 |
| 50_Y | 81_L | 2.158 | 1.00 |
| 33_T | 49_E | 1.803 | 1.00 |
| 79_K | 82_D | 1.792 | 1.00 |
| 8_V | 85_L | 1.791 | 1.00 |
| 25_E | 29_T | 1.680 | 0.99 |
| 37_D | 40_A | 1.671 | 0.99 |
| 30_A | 36_Y | 1.638 | 0.99 |
| 107_H | 111_C | 1.609 | 0.99 |
| 50_Y | 57_N | 1.580 | 0.99 |
| 21_V | 101_I | 1.580 | 0.99 |
| 31_F | 35_G | 1.494 | 0.99 |
| 73_C | 77_C | 1.492 | 0.98 |
| 18_Y | 52_L | 1.484 | 0.98 |
| 49_E | 56_N | 1.473 | 0.98 |
| 72_I | 98_K | 1.464 | 0.98 |
| 47_S | 56_N | 1.462 | 0.98 |
| 22_S | 96_L | 1.454 | 0.98 |
| 94_K | 98_K | 1.453 | 0.98 |
| 95_I | 104_W | 1.432 | 0.98 |
| 45_N | 58_K | 1.407 | 0.98 |
| 96_L | 101_I | 1.396 | 0.97 |
| 33_T | 47_S | 1.377 | 0.97 |
| 32_H | 36_Y | 1.352 | 0.97 |
| 19_G | 22_S | 1.340 | 0.96 |
| 9_F | 30_A | 1.336 | 0.96 |
| 12_L | 27_V | 1.325 | 0.96 |
| 11_K | 89_I | 1.319 | 0.96 |
| 41_I | 48_T | 1.316 | 0.96 |
| 75_I | 88_D | 1.304 | 0.96 |
| 60_W | 103_Y | 1.262 | 0.95 |
| 8_V | 30_A | 1.204 | 0.93 |
| 83_D | 86_T | 1.184 | 0.92 |
| 26_W | 47_S | 1.174 | 0.91 |
| 13_K | 20_G | 1.166 | 0.91 |
| 99_V | 103_Y | 1.157 | 0.91 |
| 90_V | 97_D | 1.125 | 0.89 |
| 42_V | 49_E | 1.124 | 0.89 |
| 55_I | 95_I | 1.124 | 0.89 |
| 25_E | 107_H | 1.122 | 0.89 |
| 75_I | 87_D | 1.115 | 0.88 |
| 71_N | 76_S | 1.103 | 0.88 |
| 30_A | 85_L | 1.099 | 0.87 |
| 14_D | 114_K | 1.099 | 0.87 |
| 107_H | 113_E | 1.093 | 0.87 |
| 33_T | 56_N | 1.091 | 0.87 |
| 100_G | 104_W | 1.091 | 0.87 |
| 75_I | 79_K | 1.061 | 0.85 |
| 61_C | 77_C | 1.047 | 0.84 |
| 93_K | 96_L | 1.045 | 0.83 |
| 32_H | 106_A | 1.044 | 0.83 |
| 5_K | 8_V | 1.029 | 0.82 |
| 47_S | 54_Q | 1.028 | 0.82 |
| 76_S | 79_K | 1.027 | 0.82 |
| 89_I | 93_K | 1.027 | 0.82 |
| 14_D | 68_H | 1.022 | 0.82 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 1b9oA | 1 | 1 | 100 | 0.128 | Contact Map |
| 1yroA | 2 | 1 | 100 | 0.132 | Contact Map |
| 1hmlA | 1 | 1 | 100 | 0.143 | Contact Map |
| 4yf2A | 3 | 0.9917 | 100 | 0.167 | Contact Map |
| 2z2fA | 1 | 0.9917 | 100 | 0.17 | Contact Map |
| 2nwdX | 1 | 0.9917 | 100 | 0.172 | Contact Map |
| 2gv0A | 1 | 0.9917 | 100 | 0.183 | Contact Map |
| 1lmqA | 1 | 0.9917 | 100 | 0.186 | Contact Map |
| 1qqyA | 1 | 0.9833 | 100 | 0.2 | Contact Map |
| 1jugA | 1 | 0.9917 | 100 | 0.21 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)